Viviana Romero Alarcon

I am a computational biologist developing open-source software and AI-assisted approaches to make phylogenetic comparative research more reproducible. I study trait evolution, ancestral states, and biodiversity conservation.

Role	Computational biologist; PhD candidate
Now	Doctoral candidate in Integrative Biosciences (Bioinformatics), University of Massachusetts Boston, working with Liam J. Revell. Participant in the Paul English Applied AI Institute.
Funding	WWF Fonseca Leadership, 2025–2026
Works in	R, Python, Bash, Shiny, team work, project management

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Research

My research connects phylogenetic comparative biology, statistical modeling, and scientific software. I focus on three questions:

Reproducible research: How can tools help researchers formulate hypotheses, document decisions, and design analyses that others can inspect and repeat?
Evolutionary inference: What information is needed to reconstruct ancestral traits, and how do statistical learning and graph neural networks compare with established methods?
Biodiversity and conservation: How do species traits and geography relate to extinction risk, particularly for mountain birds in the Northern Andes?

I also work on body-mass estimation in terror birds, comparing direct anatomical calibrations with indirect estimation approaches.

Selected software

Guane

Objective: Make phylogenetic comparative analysis available without writing code.
Method: R/Shiny platform with four modules (phylogenetic traits, ancestral states, diversification, SSE models). Interface in English, Spanish and Portuguese. Returns figures, diagnostics and editable R code.
Status: Documented, with tutorials. Open the site

phyloSophR

Objective: Help researchers formulate hypotheses and design transparent studies in phylogenetic comparative biology.
Method: A staged research plan: define a schema, build and annotate a pilot corpus, establish a benchmark, and evaluate a minimum engine against simpler baselines. Human review, simulation, and power analysis are planned later stages.
Status: In development. Project page

PhyloCrates

Objective: Sharpen a biological observation into critically examined hypotheses before anyone picks a method.
Method: A Socratic conversational agent with eight reasoning stages that ends in a structured Hypothesis Reasoning Record.
Status: Packaged for Claude Code, ChatGPT, Gemini and Gemini CLI. Open the site

Ofey

Objective: A desk companion concept for Socratic scientific discussion: exploring observations, alternative explanations, predictions, and study design.
Method: The planned prototype specializes in phylogenetic comparative biology, with a companion app for domain knowledge, voice, and personality.
Status: prototype planning.Read about Ofey

All projects, current and past.

Tools and practice

Languages	R, Python, Bash
Frameworks	Shiny
Methods	Phylogenetic comparative methods, statistical learning, Bayesian and maximum-likelihood inference, data visualization, data cleaning (GBIF)
Practice	Reproducible reports with Quarto, tutorials and workshops, open-source R packages